bugged stringlengths 4 228k | fixed stringlengths 0 96.3M | __index_level_0__ int64 0 481k |
|---|---|---|
def db_restart(): "Delete and rebuild database on the local" with settings(warn_only=True): local("rm kelpdb") local("python2.6 manage.py syncdb") local("python2.6 manage.py loaddata fixtures/*") | def db_restart(): "Delete and rebuild database on the local" with settings(warn_only=True): local("rm kelpdb") local("python2.6 manage.py syncdb --noinput") local("python2.6 manage.py loaddata fixtures/*") | 463,900 |
def restart_database(): "Delete and rebuild the database on the remote" with cd("/home/kelp/kelp"): sudo("su -c 'rm ../kelpdb' www-data") sudo("su -c './manage.py syncdb' www-data") sudo("su -c './manage.py loaddata fixtures/*' www-data)") | def restart_database(): "Delete and rebuild the database on the remote" with cd("/home/kelp/kelp"): with settings(warn_only=True): sudo("su -c 'rm ../kelpdb' www-data") sudo("su -c 'python manage.py syncdb --noinput' www-data") sudo("su -c 'python manage.py loaddata fixtures/*' www-data)") | 463,901 |
def main(argv=None, **kwargs): """Shell interface to :mod:`migrate.versioning.api`. kwargs are default options that can be overriden with passing --some_option as command line option :param disable_logging: Let migrate configure logging :type disable_logging: bool """ argv = argv or list(sys.argv[1:]) commands = list... | def main(argv=None, **kwargs): """Shell interface to :mod:`migrate.versioning.api`. kwargs are default options that can be overriden with passing --some_option as command line option :param disable_logging: Let migrate configure logging :type disable_logging: bool """ if argv is not None: argv = argv else: argv = lis... | 463,902 |
def test_type(self): """Can change a column's type""" # Entire column definition given self.table.c.data.alter(name='data', type=String(42)) self.refresh_table(self.table.name) self.assert_(isinstance(self.table.c.data.type, String)) self.assertEquals(self.table.c.data.type.length, 42) | def test_type(self): """Can change a column's type""" # Entire column definition given self.table.c.data.alter(name='data', type=String(42)) self.refresh_table(self.table.name) self.assert_(isinstance(self.table.c.data.type, String)) self.assertEquals(self.table.c.data.type.length, 42) | 463,903 |
def test_default(self): """Can change a column's server_default value (DefaultClauses only) Only DefaultClauses are changed here: others are managed by the application / by SA """ self.assertEquals(self.table.c.data.server_default.arg, 'tluafed') | def test_default(self): """Can change a column's server_default value (DefaultClauses only) Only DefaultClauses are changed here: others are managed by the application / by SA """ self.assertEquals(self.table.c.data.server_default.arg, 'tluafed') | 463,904 |
def test_null(self): """Can change a column's null constraint""" self.assertEquals(self.table.c.data.nullable, True) | def test_null(self): """Can change a column's null constraint""" self.assertEquals(self.table.c.data.nullable, True) | 463,905 |
def test_alter_metadata_deprecated(self): try: # py 2.4 compatability :-/ cw = catch_warnings(record=True) w = cw.__enter__() warnings.simplefilter("always") self.table.c.data.alter(Column('data', String(100))) | def test_alter_deprecated(self): try: # py 2.4 compatability :-/ cw = catch_warnings(record=True) w = cw.__enter__() warnings.simplefilter("always") self.table.c.data.alter(Column('data', String(100))) | 463,906 |
def test_alter_metadata(self): """Test if alter_metadata is respected""" | def test_alter_metadata(self): """Test if alter_metadata is respected""" | 463,907 |
def test_alter_returns_delta(self): """Test if alter constructs return delta""" | def test_alter_returns_delta(self): """Test if alter constructs return delta""" | 463,908 |
def __init__(self, message, category, filename, lineno, file=None, line=None): local_values = locals() for attr in self._WARNING_DETAILS: setattr(self, attr, local_values[attr]) self._category_name = category.__name__ if category else None | def __init__(self, message, category, filename, lineno, file=None, line=None): local_values = locals() for attr in self._WARNING_DETAILS: setattr(self, attr, local_values[attr]) self._category_name = category.__name__ if category else None | 463,909 |
def test_autoname_pk(self): """PrimaryKeyConstraints can guess their name if None is given""" # Don't supply a name; it should create one cons = PrimaryKeyConstraint(self.table.c.id) cons.create() self.refresh_table() if not self.url.startswith('sqlite'): # TODO: test for index for sqlite self.compare_columns_equal(con... | def test_autoname_pk(self): """PrimaryKeyConstraints can guess their name if None is given""" # Don't supply a name; it should create one cons = PrimaryKeyConstraint(self.table.c.id) cons.create() self.refresh_table() if not self.url.startswith('sqlite'): # TODO: test for index for sqlite self.compare_columns_equal(con... | 463,910 |
def load_model(dotted_name): """Import module and use module-level variable". :param dotted_name: path to model in form of string: ``some.python.module:Class`` .. versionchanged:: 0.5.4 """ if isinstance(dotted_name, basestring): if ':' not in dotted_name: # backwards compatibility warnings.warn('model should be in ... | def load_model(dotted_name): """Import module and use module-level variable". :param dotted_name: path to model in form of string: ``some.python.module:Class`` .. versionchanged:: 0.5.4 """ if isinstance(dotted_name, basestring): if ':' not in dotted_name: # backwards compatibility warnings.warn('model should be in ... | 463,911 |
def apply_diffs(self, diffs): """Populate dict and column object with new values""" self.diffs = diffs for key in self.diff_keys: if key in diffs: setattr(self.result_column, key, diffs[key]) | def apply_diffs(self, diffs): """Populate dict and column object with new values""" self.diffs = diffs for key in self.diff_keys: if key in diffs: setattr(self.result_column, key, diffs[key]) | 463,912 |
def add_to_table(self, table): if table and not self.table: self._set_parent(table) | def add_to_table(self, table): if table is not None and self.table is None: self._set_parent(table) | 463,913 |
def compare_1_column(self, col, *p, **k): """Compares one Column object""" self.table = k.pop('table', None) or col.table self.result_column = col if len(p): k = self._extract_parameters(p, k, self.result_column) return k | def compare_1_column(self, col, *p, **k): """Compares one Column object""" self.table = k.pop('table', None) if self.table is None: self.table = col.table self.result_column = col if len(p): k = self._extract_parameters(p, k, self.result_column) return k | 463,914 |
def compare_2_columns(self, old_col, new_col, *p, **k): """Compares two Column objects""" self.process_column(new_col) self.table = k.pop('table', None) or old_col.table or new_col.table self.result_column = old_col | def compare_2_columns(self, old_col, new_col, *p, **k): """Compares two Column objects""" self.process_column(new_col) self.table = k.pop('table', None) if self.table is None: self.table = old_col.table if self.table is None: new_col.table self.result_column = old_col | 463,915 |
def assert_numcols(num_of_expected_cols): # number of cols should be correct in table object and in database self.refresh_table(self.table_name) result = len(self.table.c) self.assertEquals(result, num_of_expected_cols), if col_k.get('primary_key', None): # new primary key: check its length too result = len(self.table... | def assert_numcols(num_of_expected_cols): # number of cols should be correct in table object and in database self.refresh_table(self.table_name) result = len(self.table.c) self.assertEquals(result, num_of_expected_cols), if col_k.get('primary_key', None): # new primary key: check its len... | 463,916 |
def assert_numcols(num_of_expected_cols): # number of cols should be correct in table object and in database self.refresh_table(self.table_name) result = len(self.table.c) self.assertEquals(result, num_of_expected_cols), if col_k.get('primary_key', None): # new primary key: check its length too result = len(self.table... | def assert_numcols(num_of_expected_cols): # number of cols should be correct in table object and in database self.refresh_table(self.table_name) result = len(self.table.c) self.assertEquals(result, num_of_expected_cols), if col_k.get('primary_key', None): # new primary key: check its length too result = len(self.table... | 463,917 |
def run(self, engine, step): """Core method of Script file. Exectues :func:`update` or :func:`downgrade` functions | def run(self, engine, step): """Core method of Script file. Exectues :func:`update` or :func:`downgrade` functions | 463,918 |
def test_main_with_runpy(self): if sys.version_info[:2] == (2, 4): raise SkipTest("runpy is not part of python2.4") asd try: run_module('migrate.versioning.shell', run_name='__main__') except: pass | def test_main_with_runpy(self): if sys.version_info[:2] == (2, 4): raise SkipTest("runpy is not part of python2.4") try: run_module('migrate.versioning.shell', run_name='__main__') except: pass | 463,919 |
def __init__(self, engine, repository): if isinstance(repository, str): repository = Repository(repository) self.engine = engine self.repository = repository self.meta = MetaData(engine) self.load() | def __init__(self, engine, repository): if isinstance(repository, basestring): repository = Repository(repository) self.engine = engine self.repository = repository self.meta = MetaData(engine) self.load() | 463,920 |
def verify_module(cls, path): """Ensure path is a valid script :param path: Script location :type path: string :raises: :exc:`InvalidScriptError <migrate.exceptions.InvalidScriptError>` :returns: Python module """ # Try to import and get the upgrade() func module = import_path(path) try: assert callable(module.upgrade... | def verify_module(cls, path): """Ensure path is a valid script :param path: Script location :type path: string :raises: :exc:`InvalidScriptError <migrate.exceptions.InvalidScriptError>` :returns: Python module """ # Try to import and get the upgrade() func module = import_path(path) try: assert callable(module.upgrade... | 463,921 |
def run(self, engine, step): """Core method of Script file. Exectues :func:`update` or :func:`downgrade` functions | def run(self, engine, step): """Core method of Script file. Exectues :func:`update` or :func:`downgrade` functions | 463,922 |
def run(self, engine, step): """Core method of Script file. Exectues :func:`update` or :func:`downgrade` functions | def run(self, engine, step): """Core method of Script file. Exectues :func:`update` or :func:`downgrade` functions | 463,923 |
def autoname(self): """Mimic the database's automatic constraint names""" ret = "%(table)s_%(reftable)s_fkey" % dict( table=self.table.name, reftable=self.reftable.name,) return ret | def autoname(self): """Mimic the database's automatic constraint names""" ret = "%(table)s_%(firstcolumn)s_fkey" % dict( table=self.table.name, reftable=self.reftable.name,) return ret | 463,924 |
def autoname(self): """Mimic the database's automatic constraint names""" ret = "%(table)s_%(reftable)s_fkey" % dict( table=self.table.name, reftable=self.reftable.name,) return ret | def autoname(self): """Mimic the database's automatic constraint names""" ret = "%(table)s_%(reftable)s_fkey" % dict( table=self.table.name, firstcolumn=self.columns[0],) return ret | 463,925 |
def __init__(self, record=False, module=None): """Specify whether to record warnings and if an alternative module should be used other than sys.modules['warnings']. | def __init__(self, record=False, module=None): """Specify whether to record warnings and if an alternative module should be used other than sys.modules['warnings']. | 463,926 |
def test_rundiffs_in_shell(self): # This is a variant of the test_schemadiff tests but run through the shell level. # These shell tests are hard to debug (since they keep forking processes), so they shouldn't replace the lower-level tests. repos_name = 'repos_name' repos_path = self.tmp() script_path = self.tmp_py() mo... | def test_rundiffs_in_shell(self): # This is a variant of the test_schemadiff tests but run through the shell level. # These shell tests are hard to debug (since they keep forking processes), so they shouldn't replace the lower-level tests. repos_name = 'repos_name' repos_path = self.tmp() script_path = self.tmp_py() mo... | 463,927 |
def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet ): features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} for f in HTSeq.GFF_Reader( gff_filename ): if f.iv.chrom not in features.step_vectors.keys(): features.add_chrom( f.iv.chrom ) if f.type... | def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet ): features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} for f in HTSeq.GFF_Reader( gff_filename ): if f.iv.chrom not in features.step_vectors.keys(): features.add_chrom( f.iv.chrom ) if f.type... | 463,928 |
def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet ): features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} for f in HTSeq.GFF_Reader( gff_filename ): if f.iv.chrom not in features.step_vectors.keys(): features.add_chrom( f.iv.chrom ) if f.type... | def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet ): features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} for f in HTSeq.GFF_Reader( gff_filename ): if f.iv.chrom not in features.step_vectors.keys(): features.add_chrom( f.iv.chrom ) if f.type... | 463,929 |
def __init__( self, chrom_lengths, stranded=True ): GenomicArray.__init__( self, chrom_lengths, stranded, 'O' ) for chrom in self.step_vectors: if self.stranded: self.step_vectors[ chrom ][ strand ][ 0 : chrom_lengths[chrom] ] = set() else: self.step_vectors[ chrom ][ 0 : chrom_lengths[chrom] ] = set() | def __init__( self, chrom_lengths, stranded=True ): GenomicArray.__init__( self, chrom_lengths, stranded, 'O' ) for chrom in self.step_vectors: if self.stranded: self.step_vectors[ chrom ][ "+" ][ : ] = set() self.step_vectors[ chrom ][ "-" ][ : ] = set() else: self.step_vectors[ chrom ][ 0 : chrom_lengths[chrom] ] = s... | 463,930 |
def __init__( self, chrom_lengths, stranded=True ): GenomicArray.__init__( self, chrom_lengths, stranded, 'O' ) for chrom in self.step_vectors: if self.stranded: self.step_vectors[ chrom ][ strand ][ 0 : chrom_lengths[chrom] ] = set() else: self.step_vectors[ chrom ][ 0 : chrom_lengths[chrom] ] = set() | def __init__( self, chrom_lengths, stranded=True ): GenomicArray.__init__( self, chrom_lengths, stranded, 'O' ) for chrom in self.step_vectors: if self.stranded: self.step_vectors[ chrom ][ strand ][ 0 : chrom_lengths[chrom] ] = set() else: self.step_vectors[ chrom ][ : ] = set() | 463,931 |
def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet ): features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} # Try to open samfile to fail early in case it is not there open( sam_filename ).close() for f in HTSeq.GFF_Reader( gff_filename ): if ... | def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet ): features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} # Try to open samfile to fail early in case it is not there open( sam_filename ).close() for f in HTSeq.GFF_Reader( gff_filename ): if ... | 463,932 |
def main(): optParser = optparse.OptionParser( usage = "%prog [options] sam_file gff_file", description= "This script takes an alignment file in SAM format and a " + "feature file in GFF format and calculates for each feature " + "the number of reads mapping to it. See " + "http://www-huber.embl.de/users/anders/HTSe... | def main(): optParser = optparse.OptionParser( usage = "%prog [options] sam_file gff_file", description= "This script takes an alignment file in SAM format and a " + "feature file in GFF format and calculates for each feature " + "the number of reads mapping to it. See " + "http://www-huber.embl.de/users/anders/HTSe... | 463,933 |
def main(): optParser = optparse.OptionParser( usage = "%prog [options] sam_file gff_file", description= "This script takes an alignment file in SAM format and a " + "feature file in GFF format and calculates for each feature " + "the number of reads mapping to it. See " + "http://www-huber.embl.de/users/anders/HTSe... | def main(): optParser = optparse.OptionParser( usage = "%prog [options] sam_file gff_file", description= "This script takes an alignment file in SAM format and a " + "feature file in GFF format and calculates for each feature " + "the number of reads mapping to it. See " + "http://www-huber.embl.de/users/anders/HTSe... | 463,934 |
def main(): optParser = optparse.OptionParser( usage = "%prog [options] sam_file gff_file", description= "This script takes an alignment file in SAM format and a " + "feature file in GFF format and calculates for each feature " + "the number of reads mapping to it. See " + "http://www-huber.embl.de/users/anders/HTSe... | def main(): optParser = optparse.OptionParser( usage = "%prog [options] sam_file gff_file", description= "This script takes an alignment file in SAM format and a " + "feature file in GFF format and calculates for each feature " + "the number of reads mapping to it. See " + "http://www-huber.embl.de/users/anders/HTSe... | 463,935 |
def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet, minaqual ): if quiet: warnings.filterwarnings( action="ignore", module="HTSeq" ) features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} # Try to open samfile to fail early in case it is not th... | defexcept: sys.stderr.write( "Error occured when reading first line of sam file." ) raise try: count_reads_in_features(except: sys.stderr.write( "Error occured when reading first line of sam file." ) raise try: sam_filename,except: sys.stderr.write( "Error occured when reading first line of sam file." ) raise try: g... | 463,936 |
def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet, minaqual ): if quiet: warnings.filterwarnings( action="ignore", module="HTSeq" ) features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} # Try to open samfile to fail early in case it is not th... | def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet, minaqual ): if quiet: warnings.filterwarnings( action="ignore", module="HTSeq" ) features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} # Try to open samfile to fail early in case it is not th... | 463,937 |
def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet, minaqual ): if quiet: warnings.filterwarnings( action="ignore", module="HTSeq" ) features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} # Try to open samfile to fail early in case it is not th... | def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet, minaqual ): if quiet: warnings.filterwarnings( action="ignore", module="HTSeq" ) features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} # Try to open samfile to fail early in case it is not th... | 463,938 |
def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet ): features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} for f in HTSeq.GFF_Reader( gff_filename ): if f.iv.chrom not in features.step_vectors.keys(): features.add_chrom( f.iv.chrom ) if f.type... | def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet ): features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} for f in HTSeq.GFF_Reader( gff_filename ): if f.iv.chrom not in features.step_vectors.keys(): features.add_chrom( f.iv.chrom ) if f.type... | 463,939 |
def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet ): features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} for f in HTSeq.GFF_Reader( gff_filename ): if f.iv.chrom not in features.step_vectors.keys(): features.add_chrom( f.iv.chrom ) if f.type... | defcount_reads_in_features(sam_filename,gff_filename,stranded,overlap_mode,feature_type,id_attribute,quiet):features=HTSeq.GenomicArrayOfSets([],stranded)counts={}forfinHTSeq.GFF_Reader(gff_filename):iff.iv.chromnotinfeatures.step_vectors.keys():features.add_chrom(f.iv.chrom)iff.type==feature_type:try:features.add_valu... | 463,940 |
def main(): optParser = optparse.OptionParser( usage = "%prog [options] sam_file gff_file", description= "This script takes an alignment file in SAM format and a " + "feature file in GFF format and calculates for each feature " + "the number of reads mapping to it. See " + "http://www-huber.embl.de/users/anders/HTSeq... | def main(): optParser = optparse.OptionParser( usage = "%prog [options] sam_file gff_file", description= "This script takes an alignment file in SAM format and a " + "feature file in GFF format and calculates for each feature " + "the number of reads mapping to it. See " + "http://www-huber.embl.de/users/anders/HTSeq... | 463,941 |
def my_showwarning( message, category, filename, lineno = None, line = None ): sys.stderr.write( "Warning: %s\n" % message ) | def my_showwarning( message, category, filename, lineno = None, line = None ): sys.stderr.write( "Warning: %s\n" % message ) | 463,942 |
def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet ): features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} for f in HTSeq.GFF_Reader( gff_filename ): if f.iv.chrom not in features.step_vectors.keys(): features.add_chrom( f.iv.chrom ) if f.type... | def count_reads_in_features( sam_filename, gff_filename, stranded, overlap_mode, feature_type, id_attribute, quiet ): features = HTSeq.GenomicArrayOfSets( [], stranded ) counts = {} for f in HTSeq.GFF_Reader( gff_filename ): if f.iv.chrom not in features.step_vectors.keys(): features.add_chrom( f.iv.chrom ) if f.type... | 463,943 |
def parse_GFF_attribute_string( attrStr, extra_return_first_value=False ): """Parses a GFF attribute string and returns it as a dictionary. If 'extra_return_first_value' is set, a pair is returned: the dictionary and the value of the first attribute. This might be useful if this is the ID. """ if attrStr.endswith( "\n... | def parse_GFF_attribute_string( attrStr, extra_return_first_value=False ): """Parses a GFF attribute string and returns it as a dictionary. If 'extra_return_first_value' is set, a pair is returned: the dictionary and the value of the first attribute. This might be useful if this is the ID. """ if attrStr.endswith( "\n... | 463,944 |
def get_sequence_lengths( self ): seqname = None seqlengths = {} for line in FileOrSequence.__iter__( self ): if line.startswith( ">" ): if seqname is not None: seqlengths[ seqname ] = length print seqname, length mo = _re_fasta_header_line.match( line ) seqname = mo.group(1) length = 0 else: assert seqname is not None... | def get_sequence_lengths( self ): seqname = None seqlengths = {} for line in FileOrSequence.__iter__( self ): if line.startswith( ">" ): if seqname is not None: seqlengths[ seqname ] = length mo = _re_fasta_header_line.match( line ) seqname = mo.group(1) length = 0 else: assert seqname is not None, "FASTA file does not... | 463,945 |
def __iter__( self ): for line in FileOrSequence.__iter__( self ): if line.startswith( "@" ): # do something with the header line pass | def __iter__( self ): for line in FileOrSequence.__iter__( self ): if line.startswith( "@" ): # do something with the header line pass | 463,946 |
def __init__( self, dict chrom_lengths, bool stranded=True ): GenomicArray.__init__( self, chrom_lengths, stranded, 'O' ) for chrom in self.step_vectors: if self.stranded: self.step_vectors[ chrom ][ strand ][ 0 : self.chrom_lengths[chrom] ] = set() else: self.step_vectors[ chrom ][ 0 : self.chrom_lengths[chrom] ] = se... | def __init__( self, chrom_lengths, stranded=True ): GenomicArray.__init__( self, chrom_lengths, stranded, 'O' ) for chrom in self.step_vectors: if self.stranded: self.step_vectors[ chrom ][ strand ][ 0 : self.chrom_lengths[chrom] ] = set() else: self.step_vectors[ chrom ][ 0 : self.chrom_lengths[chrom] ] = set() | 463,947 |
def __init__( self, dict chrom_lengths, bool stranded=True ): GenomicArray.__init__( self, chrom_lengths, stranded, 'O' ) for chrom in self.step_vectors: if self.stranded: self.step_vectors[ chrom ][ strand ][ 0 : self.chrom_lengths[chrom] ] = set() else: self.step_vectors[ chrom ][ 0 : self.chrom_lengths[chrom] ] = se... | def __init__( self, dict chrom_lengths, bool stranded=True ): GenomicArray.__init__( self, chrom_lengths, stranded, 'O' ) for chrom in self.step_vectors: if self.stranded: self.step_vectors[ chrom ][ strand ][ 0 : chrom_lengths[chrom] ] = set() else: self.step_vectors[ chrom ][ 0 : self.chrom_lengths[chrom] ] = set() | 463,948 |
def __init__( self, dict chrom_lengths, bool stranded=True ): GenomicArray.__init__( self, chrom_lengths, stranded, 'O' ) for chrom in self.step_vectors: if self.stranded: self.step_vectors[ chrom ][ strand ][ 0 : self.chrom_lengths[chrom] ] = set() else: self.step_vectors[ chrom ][ 0 : self.chrom_lengths[chrom] ] = se... | def __init__( self, dict chrom_lengths, bool stranded=True ): GenomicArray.__init__( self, chrom_lengths, stranded, 'O' ) for chrom in self.step_vectors: if self.stranded: self.step_vectors[ chrom ][ strand ][ 0 : self.chrom_lengths[chrom] ] = set() else: self.step_vectors[ chrom ][ 0 : chrom_lengths[chrom] ] = set() | 463,949 |
def _f( oldset ): newset = set.copy() newset.add( value ) return newset | def _f( oldset ): newset = oldset.copy() newset.add( value ) return newset | 463,950 |
def main(): optParser = optparse.OptionParser( usage = "%prog [options] sam_file gff_file", description= "This script takes an alignment file in SAM format and a " + "feature file in GFF format and calculates for each feature " + "the number of reads mapping to it. See " + "http://www-huber.embl.de/users/anders/HTSe... | def main(): optParser = optparse.OptionParser( usage = "%prog [options] sam_file gff_file", description= "This script takes an alignment file in SAM format and a " + "feature file in GFF format and calculates for each feature " + "the number of reads mapping to it. See " + "http://www-huber.embl.de/users/anders/HTSe... | 463,951 |
def doLock(self, lockfile = YUM_PID_FILE): """perform the yum locking, raise yum-based exceptions, not OSErrors""" # if we're not root then we don't lock - just return nicely if self.conf.uid != 0: return root = self.conf.installroot lockfile = root + '/' + lockfile # lock in the chroot lockfile = os.path.normpath(lo... | def doLock(self, lockfile = YUM_PID_FILE): """perform the yum locking, raise yum-based exceptions, not OSErrors""" # if we're not root then we don't lock - just return nicely if self.conf.uid != 0: return root = self.conf.installroot lockfile = root + '/' + lockfile # lock in the chroot lockfile = os.path.normpath(lo... | 463,952 |
def _ftype(mode): """ Given a "mode" return the name of the type of file. """ if stat.S_ISREG(mode): return "file" if stat.S_ISDIR(mode): return "directory" if stat.S_ISLNK(mode): return "symlink" if stat.S_ISFIFO(mode): return "fifo" if stat.S_ISCHR(mode): return "character device" if stat.S_ISBLK(mode): return "... | def _ftype(mode): """ Given a "mode" return the name of the type of file. """ if stat.S_ISREG(mode): return "file" if stat.S_ISDIR(mode): return "directory" if stat.S_ISLNK(mode): return "symlink" if stat.S_ISFIFO(mode): return "fifo" if stat.S_ISCHR(mode): return "character device" if stat.S_ISBLK(mode): return "... | 463,953 |
def _ftype(mode): """ Given a "mode" return the name of the type of file. """ if stat.S_ISREG(mode): return "file" if stat.S_ISDIR(mode): return "directory" if stat.S_ISLNK(mode): return "symlink" if stat.S_ISFIFO(mode): return "fifo" if stat.S_ISCHR(mode): return "character device" if stat.S_ISBLK(mode): return "... | def _ftype(mode): """ Given a "mode" return the name of the type of file. """ if stat.S_ISREG(mode): return "file" if stat.S_ISDIR(mode): return "directory" if stat.S_ISLNK(mode): return "symlink" if stat.S_ISFIFO(mode): return "fifo" if stat.S_ISCHR(mode): return "character device" if stat.S_ISBLK(mode): return "... | 463,954 |
def remove(self, po=None, **kwargs): """try to find and mark for remove the specified package(s) - if po is specified then that package object (if it is installed) will be marked for removal. if no po then look at kwargs, if neither then raise an exception""" | def remove(self, po=None, **kwargs): """try to find and mark for remove the specified package(s) - if po is specified then that package object (if it is installed) will be marked for removal. if no po then look at kwargs, if neither then raise an exception""" | 463,955 |
def _get_cached_simpleVersion_main(self): """ Return the cached string of the main rpmdbv. """ if self._have_cached_rpmdbv_data is not None: return self._have_cached_rpmdbv_data | def _get_cached_simpleVersion_main(self): """ Return the cached string of the main rpmdbv. """ if self._have_cached_rpmdbv_data is not None: return self._have_cached_rpmdbv_data | 463,956 |
def _get_cached_simpleVersion_main(self): """ Return the cached string of the main rpmdbv. """ if self._have_cached_rpmdbv_data is not None: return self._have_cached_rpmdbv_data | def _get_cached_simpleVersion_main(self): """ Return the cached string of the main rpmdbv. """ if self._have_cached_rpmdbv_data is not None: return self._have_cached_rpmdbv_data | 463,957 |
def firstParse(self,args): # Parse only command line options that affect basic yum setup try: args = _filtercmdline( ('--noplugins','--version','-q', '-v', "--quiet", "--verbose"), ('-c', '-d', '-e', '--installroot', '--disableplugin', '--enableplugin', '--releasever', '--setopt'), args) except ValueError, arg: self.ba... | def firstParse(self,args): # Parse only command line options that affect basic yum setup try: args = _filtercmdline( ('--noplugins','--version','-q', '-v', "--quiet", "--verbose"), ('-c', '--config', '-d', '--debuglevel', '-e', '--errorlevel', '--installroot', '--disableplugin', '--enableplugin', '--releasever', '--set... | 463,958 |
def historyListCmd(self, extcmds): """ Shows the user a list of data about the history. """ | def historyListCmd(self, extcmds): """ Shows the user a list of data about the history. """ | 463,959 |
def historyAddonInfoCmd(self, extcmds): tid = None if len(extcmds) > 1: tid = extcmds[1] try: int(tid) except ValueError: self.logger.critical(_('No transaction ID given')) return 1, ['Failed history addon-info'] except TypeError: pass # No tid arg. passed, use last... | def historyAddonInfoCmd(self, extcmds): tid = None if len(extcmds) > 1: tid = extcmds[1] if tid == 'last': tid = None if tid is not None: try: int(tid) except ValueError: self.logger.critical(_('Bad transaction ID given')) return 1, ['Failed history addon-info'] # No tid arg. passed, use last... | 463,960 |
def getArchList(thisarch=None): # this returns a list of archs that are compatible with arch given if not thisarch: thisarch = canonArch archlist = [thisarch] while thisarch in arches: thisarch = arches[thisarch] archlist.append(thisarch) # hack hack hack # sparc64v is also sparc64 compat if archlist[0] == "sparc64v"... | defdef _try_read_cpuinfo(): """ Try to read /proc/cpuinfo ... if we can't ignore errors (ie. proc not mounted). """ try: lines = open("/proc/cpuinfo", "r").readlines() return lines except: return [] getArchList(thisarch=None):def _try_read_cpuinfo(): """ Try to read /proc/cpuinfo ... if we can't ignore errors (ie. proc... | 463,961 |
def getCanonX86Arch(arch): # if arch == "i586": f = open("/proc/cpuinfo", "r") lines = f.readlines() f.close() for line in lines: if line.startswith("model name") and line.find("Geode(TM)") != -1: return "geode" return arch # only athlon vs i686 isn't handled with uname currently if arch != "i686": return arch # if we... | def getCanonX86Arch(arch): # if arch == "i586": for line in _try_read_cpuinfo(): if line.startswith("model name") and line.find("Geode(TM)") != -1: return "geode" return arch # only athlon vs i686 isn't handled with uname currently if arch != "i686": return arch # if we're i686 and AuthenticAMD, then we should be an a... | 463,962 |
def getCanonX86Arch(arch): # if arch == "i586": f = open("/proc/cpuinfo", "r") lines = f.readlines() f.close() for line in lines: if line.startswith("model name") and line.find("Geode(TM)") != -1: return "geode" return arch # only athlon vs i686 isn't handled with uname currently if arch != "i686": return arch # if we... | def getCanonX86Arch(arch): # if arch == "i586": for line in _try_read_cpuinfo(): if line.startswith("model name") and line.find("Geode(TM)") != -1: return "geode" return arch # only athlon vs i686 isn't handled with uname currently if arch != "i686": return arch # if we're i686 and AuthenticAMD, then we should be an a... | 463,963 |
def getCanonPPCArch(arch): # FIXME: should I do better handling for mac, etc? if arch != "ppc64": return arch machine = None f = open("/proc/cpuinfo", "r") lines = f.readlines() f.close() for line in lines: if line.find("machine") != -1: machine = line.split(':')[1] break if machine is None: return arch if machine.fi... | def getCanonPPCArch(arch): # FIXME: should I do better handling for mac, etc? if arch != "ppc64": return arch machine = None for line in _try_read_cpuinfo(): if line.find("machine") != -1: machine = line.split(':')[1] break if machine is None: return arch if machine.find("CHRP IBM") != -1: return "ppc64pseries" if ma... | 463,964 |
def getCanonSPARCArch(arch): # Deal with sun4v, sun4u, sun4m cases SPARCtype = None f = open("/proc/cpuinfo", "r") lines = f.readlines() f.close() for line in lines: if line.startswith("type"): SPARCtype = line.split(':')[1] break if SPARCtype is None: return arch if SPARCtype.find("sun4v") != -1: if arch.startswith("... | def getCanonSPARCArch(arch): # Deal with sun4v, sun4u, sun4m cases SPARCtype = None for line in _try_read_cpuinfo(): if line.startswith("type"): SPARCtype = line.split(':')[1] break if SPARCtype is None: return arch if SPARCtype.find("sun4v") != -1: if arch.startswith("sparc64"): return "sparc64v" else: return "sparcv... | 463,965 |
def getCanonX86_64Arch(arch): if arch != "x86_64": return arch vendor = None f = open("/proc/cpuinfo", "r") lines = f.readlines() f.close() for line in lines: if line.startswith("vendor_id"): vendor = line.split(':')[1] break if vendor is None: return arch if vendor.find("Authentic AMD") != -1 or vendor.find("Authent... | def getCanonX86_64Arch(arch): if arch != "x86_64": return arch vendor = None for line in _try_read_cpuinfo(): if line.startswith("vendor_id"): vendor = line.split(':')[1] break if vendor is None: return arch if vendor.find("Authentic AMD") != -1 or vendor.find("AuthenticAMD") != -1: return "amd64" if vendor.find("Gen... | 463,966 |
def write_addon_data(self, dataname, data): """append data to an arbitrary-named file in the history addon_path/transaction id location, returns True if write succeeded, False if not""" if not hasattr(self, '_tid'): # maybe we should raise an exception or a warning here? return False if not dataname: return False if... | def write_addon_data(self, dataname, data): """append data to an arbitrary-named file in the history addon_path/transaction id location, returns True if write succeeded, False if not""" if not hasattr(self, '_tid'): # maybe we should raise an exception or a warning here? return False if not dataname: return False if... | 463,967 |
def runTransaction(self, cb): """takes an rpm callback object, performs the transaction""" | def runTransaction(self, cb): """takes an rpm callback object, performs the transaction""" | 463,968 |
def _apply_installroot(yumconf, option): path = getattr(yumconf, option) ir_path = yumconf.installroot + path ir_path = ir_path.replace('//', '/') # os.path.normpath won't fix this and # it annoys me ir_path = varReplace(ir_path, yumvars) setattr(yumconf, option, ir_path) | def _apply_installroot(yumconf, option): path = getattr(yumconf, option) ir_path = yumconf.installroot + path ir_path = ir_path.replace('//', '/') # os.path.normpath won't fix this and # it annoys me ir_path = varReplace(ir_path, yumvars) setattr(yumconf, option, ir_path) | 463,969 |
def _sort_and_filter_installonly(pkgs): """ Allow the admin to specify some overrides fo installonly pkgs. using the yumdb. """ ret_beg = [] ret_mid = [] ret_end = [] for pkg in sorted(pkgs): if 'installonly' not in pkg.yumdb_info: ret_mid.append(pkg) continue | def _sort_and_filter_installonly(pkgs): """ Allow the admin to specify some overrides fo installonly pkgs. using the yumdb. """ ret_beg = [] ret_mid = [] ret_end = [] for pkg in sorted(pkgs): if 'installonly' not in pkg.yumdb_info: ret_mid.append(pkg) continue | 463,970 |
def getReposFromConfigFile(self, repofn, repo_age=None, validate=None): """read in repositories from a config .repo file""" | def getReposFromConfigFile(self, repofn, repo_age=None, validate=None): """read in repositories from a config .repo file""" | 463,971 |
def _pkg2obspkg(self, po): """ Given a package return the package it's obsoleted by and so we should install instead. Or None if there isn't one. """ thispkgobsdict = self.up.checkForObsolete([po.pkgtup]) if po.pkgtup in thispkgobsdict: obsoleting = thispkgobsdict[po.pkgtup] oobsoleting = [] # We want to keep the arch... | def _pkg2obspkg(self, po): """ Given a package return the package it's obsoleted by and so we should install instead. Or None if there isn't one. """ thispkgobsdict = self.up.checkForObsolete([po.pkgtup]) if po.pkgtup in thispkgobsdict: obsoleting = thispkgobsdict[po.pkgtup] oobsoleting = [] # We want to keep the arch... | 463,972 |
def testMultiLibUpdate(self): ''' foo-1.i386 & foo-1.xf86_64 is updated by foo-2.i386 & foo-2.xf86_64 foo-2.xf86_64 has a missing req, and get skipped, foo-2.i386 has to be skipped to or it will fail in the rpm test transaction ''' ipo1 = self.instPackage('foo', '1',arch='i386') ipo2 = self.instPackage('foo', '1',arch=... | def testMultiLibUpdate(self): ''' foo-1.i386 & foo-1.x86_64 is updated by foo-2.i386 & foo-2.x86_64 foo-2.x86_64 has a missing req, and gets skipped, foo-2.i386 has to be skipped too or it will fail in the rpm test transaction ''' ipo1 = self.instPackage('foo', '1',arch='i386') ipo2 = self.instPackage('foo', '1',arch='... | 463,973 |
def _printTransaction(self): #transaction set states state = { TS_UPDATE : "update", TS_INSTALL : "install", TS_TRUEINSTALL: "trueinstall", TS_ERASE : "erase", TS_OBSOLETED : "obsoleted", TS_OBSOLETING : "obsoleting", TS_AVAILABLE : "available", TS_UPDATED : "updated"} | def _printTransaction(self): #transaction set states state = { TS_UPDATE : "update", TS_INSTALL : "install", TS_TRUEINSTALL: "trueinstall", TS_ERASE : "erase", TS_OBSOLETED : "obsoleted", TS_OBSOLETING : "obsoleting", TS_AVAILABLE : "available", TS_UPDATED : "updated"} | 463,974 |
def _printTransaction(self): #transaction set states state = { TS_UPDATE : "update", TS_INSTALL : "install", TS_TRUEINSTALL: "trueinstall", TS_ERASE : "erase", TS_OBSOLETED : "obsoleted", TS_OBSOLETING : "obsoleting", TS_AVAILABLE : "available", TS_UPDATED : "updated"} | def _printTransaction(self): #transaction set states state = { TS_UPDATE : "update", TS_INSTALL : "install", TS_TRUEINSTALL: "trueinstall", TS_ERASE : "erase", TS_OBSOLETED : "obsoleted", TS_OBSOLETING : "obsoleting", TS_AVAILABLE : "available", TS_UPDATED : "updated"} | 463,975 |
def testRLDaplMessWeirdInst3(self): rps, aps, ret, all = self._helperRLDaplMess() res, msg = self.runOperation(['install', 'dapl-2.0.15'], rps, aps) | def testRLDaplMessWeirdInst3(self): rps, aps, ret, all = self._helperRLDaplMess() res, msg = self.runOperation(['install', 'dapl-2.0.15'], rps, aps) | 463,976 |
def testRLDaplMessWeirdUp3(self): rps, aps, ret, all = self._helperRLDaplMess() res, msg = self.runOperation(['update', 'dapl-2.0.15'], rps, aps) | def testRLDaplMessWeirdUp3(self): rps, aps, ret, all = self._helperRLDaplMess() res, msg = self.runOperation(['update', 'dapl-2.0.15'], rps, aps) | 463,977 |
def _dump_format_items(self): msg = " <format>\n" if self.license: msg += """ <rpm:license>%s</rpm:license>\n""" % misc.to_xml(self.license) else: msg += """ <rpm:license/>\n""" if self.vendor: msg += """ <rpm:vendor>%s</rpm:vendor>\n""" % misc.to_xml(self.vendor) else: msg += """ <rpm:vendor/>\n""" if s... | def _dump_format_items(self): msg = " <format>\n" if self.license: msg += """ <rpm:license>%s</rpm:license>\n""" % misc.to_xml(self.license) else: msg += """ <rpm:license/>\n""" if self.vendor: msg += """ <rpm:vendor>%s</rpm:vendor>\n""" % misc.to_xml(self.vendor) else: msg += """ <rpm:vendor/>\n""" if s... | 463,978 |
def _dump_files(self, primary=False): msg ="" if not primary: files = self.returnFileEntries('file') dirs = self.returnFileEntries('dir') ghosts = self.returnFileEntries('ghost') else: files = self.returnFileEntries('file', primary_only=True) dirs = self.returnFileEntries('dir', primary_only=True) ghosts = self.returnF... | def _dump_files(self, primary=False): msg ="\n" if not primary: files = self.returnFileEntries('file') dirs = self.returnFileEntries('dir') ghosts = self.returnFileEntries('ghost') else: files = self.returnFileEntries('file', primary_only=True) dirs = self.returnFileEntries('dir', primary_only=True) ghosts = self.retur... | 463,979 |
def search(self, patterns, ignore_case=True): """ Search for history transactions which contain specified packages al. la. "yum list". Returns transaction ids. """ # Search packages ... kind of sucks that it's search not list, pkglist? | def search(self, patterns, ignore_case=True): """ Search for history transactions which contain specified packages al. la. "yum list". Returns transaction ids. """ # Search packages ... kind of sucks that it's search not list, pkglist? | 463,980 |
def __init__(self,name,ver,usage): YumBaseCli.__init__(self) self._parser = YumOptionParser(base=self,utils=True,usage=usage) self._usage = usage self._utilName = name self._utilVer = ver self._option_group = OptionGroup(self._parser, "%s options" % self._utilName,"") self._parser.add_option_group(self._option_group) s... | def def exUserCancel(self): self.logger.critical(_('\n\nExiting on user cancel')) if self.unlock(): return 200 return 1 def exIOError(self, e): if e.errno == 32: self.logger.critical(_('\n\nExiting on Broken Pipe')) else: self.logger.critical(_('\n\n%s') % str(e)) if self.unlock(): return 200 return 1 def exPluginExi... | 463,981 |
def doUtilYumSetup(self): """do a default setup for all the normal/necessary yum components, really just a shorthand for testing""" # FIXME - we need another way to do this, I think. try: self.waitForLock() self._getTs() self._getRpmDB() self._getRepos(doSetup = True) self._getSacks() except Errors.YumBaseError, msg: s... | def def doUtilBuildTransaction(self): try: (result, resultmsgs) = self.buildTransaction() except plugins.PluginYumExit, e: return self.exPluginExit(e) except Errors.YumBaseError, e: result = 1 resultmsgs = [unicode(e)] except KeyboardInterrupt: return self.exUserCancel() except IOError, e: return self.exIOError(e) if... | 463,982 |
def exUserCancel(): self.logger.critical(_('\n\nExiting on user cancel')) if unlock(): return 200 return 1 | def exUserCancel(): self.logger.critical(_('\n\nExiting on user cancel')) if unlock(): return 200 return 1 | 463,983 |
def unlock(): try: self.closeRpmDB() self.doUnlock() except Errors.LockError, e: return 200 return 0 | def unlock(): try: self.closeRpmDB() self.doUnlock() except Errors.LockError, e: return 200 return 0 | 463,984 |
def unlock(): try: self.closeRpmDB() self.doUnlock() except Errors.LockError, e: return 200 return 0 | def unlock(): try: self.closeRpmDB() self.doUnlock() except Errors.LockError, e: return 200 return 0 | 463,985 |
def unlock(): try: self.closeRpmDB() self.doUnlock() except Errors.LockError, e: return 200 return 0 | def unlock(): try: self.closeRpmDB() self.doUnlock() except Errors.LockError, e: return 200 return 0 | 463,986 |
def unlock(): try: self.closeRpmDB() self.doUnlock() except Errors.LockError, e: return 200 return 0 | def unlock(): try: self.closeRpmDB() self.doUnlock() except Errors.LockError, e: return 200 return 0 | 463,987 |
def unlock(): try: self.closeRpmDB() self.doUnlock() except Errors.LockError, e: return 200 return 0 | def unlock(): try: self.closeRpmDB() self.doUnlock() except Errors.LockError, e: return 200 return 0 | 463,988 |
def update(self, po=None, requiringPo=None, **kwargs): """try to mark for update the item(s) specified. po is a package object - if that is there, mark it for update, if possible else use **kwargs to match the package needing update if nothing is specified at all then attempt to update everything returns the list of t... | def update(self, po=None, requiringPo=None, **kwargs): """try to mark for update the item(s) specified. po is a package object - if that is there, mark it for update, if possible else use **kwargs to match the package needing update if nothing is specified at all then attempt to update everything returns the list of t... | 463,989 |
def update(self, po=None, requiringPo=None, **kwargs): """try to mark for update the item(s) specified. po is a package object - if that is there, mark it for update, if possible else use **kwargs to match the package needing update if nothing is specified at all then attempt to update everything returns the list of t... | def update(self, po=None, requiringPo=None, **kwargs): """try to mark for update the item(s) specified. po is a package object - if that is there, mark it for update, if possible else use **kwargs to match the package needing update if nothing is specified at all then attempt to update everything returns the list of t... | 463,990 |
def update(self, po=None, requiringPo=None, **kwargs): """try to mark for update the item(s) specified. po is a package object - if that is there, mark it for update, if possible else use **kwargs to match the package needing update if nothing is specified at all then attempt to update everything returns the list of t... | def update(self, po=None, requiringPo=None, **kwargs): """try to mark for update the item(s) specified. po is a package object - if that is there, mark it for update, if possible else use **kwargs to match the package needing update if nothing is specified at all then attempt to update everything returns the list of t... | 463,991 |
def update(self, po=None, requiringPo=None, **kwargs): """try to mark for update the item(s) specified. po is a package object - if that is there, mark it for update, if possible else use **kwargs to match the package needing update if nothing is specified at all then attempt to update everything returns the list of t... | def update(self, po=None, requiringPo=None, **kwargs): """try to mark for update the item(s) specified. po is a package object - if that is there, mark it for update, if possible else use **kwargs to match the package needing update if nothing is specified at all then attempt to update everything returns the list of t... | 463,992 |
def update(self, po=None, requiringPo=None, **kwargs): """try to mark for update the item(s) specified. po is a package object - if that is there, mark it for update, if possible else use **kwargs to match the package needing update if nothing is specified at all then attempt to update everything returns the list of t... | def update(self, po=None, requiringPo=None, **kwargs): """try to mark for update the item(s) specified. po is a package object - if that is there, mark it for update, if possible else use **kwargs to match the package needing update if nothing is specified at all then attempt to update everything returns the list of t... | 463,993 |
def update(self, po=None, requiringPo=None, **kwargs): """try to mark for update the item(s) specified. po is a package object - if that is there, mark it for update, if possible else use **kwargs to match the package needing update if nothing is specified at all then attempt to update everything returns the list of t... | def update(self, po=None, requiringPo=None, **kwargs): """try to mark for update the item(s) specified. po is a package object - if that is there, mark it for update, if possible else use **kwargs to match the package needing update if nothing is specified at all then attempt to update everything returns the list of t... | 463,994 |
def update(self, po=None, requiringPo=None, **kwargs): """try to mark for update the item(s) specified. po is a package object - if that is there, mark it for update, if possible else use **kwargs to match the package needing update if nothing is specified at all then attempt to update everything returns the list of t... | def update(self, po=None, requiringPo=None, **kwargs): """try to mark for update the item(s) specified. po is a package object - if that is there, mark it for update, if possible else use **kwargs to match the package needing update if nothing is specified at all then attempt to update everything returns the list of t... | 463,995 |
def _iter_two_pkgs(self, ignore): last = None for pkg in sorted(self.returnPackages()): if pkg.name in ignore: continue if last is None: last = pkg continue yield last, pkg last = pkg | def _iter_two_pkgs(self, ignore_provides): last = None for pkg in sorted(self.returnPackages()): if pkg.name in ignore: continue if last is None: last = pkg continue yield last, pkg last = pkg | 463,996 |
def _iter_two_pkgs(self, ignore): last = None for pkg in sorted(self.returnPackages()): if pkg.name in ignore: continue if last is None: last = pkg continue yield last, pkg last = pkg | def _iter_two_pkgs(self, ignore): last = None for pkg in sorted(self.returnPackages()): if pkg.name in ignore_provides: continue if ignore_provides.intersection(set(pkg.provides_names)): continue if last is None: last = pkg continue yield last, pkg last = pkg | 463,997 |
def check_duplicates(self, ignore=[]): """ Checks for any missing dependencies. """ | def check_duplicates(self, ignore=[]): """ Checks for any missing dependencies. """ | 463,998 |
def check_duplicates(self, ignore=[]): """ Checks for any missing dependencies. """ | def check_duplicates(self, ignore=[]): """ Checks for any missing dependencies. """ | 463,999 |
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